Refining the CTF
The automated defocus search used in 2dx is based entirely on ctffind2 (Grigorieff) and will find the CTF in a majority of cases. However when vibration or other distorting factors destroy parts of the CTF, or in cases where the fit is imprecise, it may be desirable to fit this manually.
To do so, select either the option from the Navigator menu or press the keyboard shortcut c. The parameters which are displayed in the defocus window allow intuitive refinement of the defocus in the x and y directions as well as refining the angle of astigmatism. This refinement of the overall defocus is achieved by altering linear combinations of Defocus X and Defocus Y in the following way:
Defocus = (DefocusX + DefocusY) / 2
Astigmatism = DefocusX - DefocusY
This allows the defocus to control the overall size (larger values result in zero-crossings closer to the origin) and the Astigmatism to control the relative proportion of Defocus in the two directions. The astigmatic angle remains the same in both cases.
Fitting the CTF does not change the original values of Defocus X and Y, but instead presents a candidate CTF based on the current values. The stored CTF may be reloaded at any time by clicking Reload. Similarly when the parameters produce an acceptable candidate CTF click Accept to replaced the stored data with the current values.